Re: [ccp4bb] Computer hardware and OS "survey"
On May 3, 2009, at 16:54, Nicholas M Glykos wrote: These Greeks ... Beware of Geeks baring Vista ... ... oh, sorry, it was gReeks? beware of them in European basketball finals then... ;-) However, the inhabitants of this planet seem to be quite fond of this OS That's because the inhabitants of this planet use computing machines mainly to play Doom & World of Warcraft ;-) Yep - a serious advantage of the W-platform compared to OSX ;-) But then it comes to using computers for actual computation, things change: ... hmmm ... However, most actual crystallographic computing I do, has very similar demands to Doom ... I would not say the same for MD though Niko ;-) A.
[ccp4bb] Applications invited for PhD Projects in Structural Biology at the University of Auckland, New Zealand
PhD Scholarships available in Structural Biology in the School of Biological Sciences at the University of Auckland, New Zealand Applications are invited for PhD scholarships in the following areas: The structure of insecticidal toxins from Yersinia entomophaga. (Dr. Shaun Lott, Dr Mark Hurst, Biocontrol and Biosecurity, AgResearch) The insecticidal tc toxins produced by a number of bacteria form large (~2.5MDa) complexes, where the assembly of up to seven proteins are required to show full insecticidal activity. The general architecture of these complexes has previously been established using single- particle EM analysis, but the structural details of the complexes, and their mode of action, remain obscure. This project aims to elucidate the structures and functions of components of the tc toxin complex from the bacterium Yersinia entomophaga. Drug targets from M. tuberculosis. (Dr. Shaun Lott, Professor Ted Baker) We have recently solved the structure of several enzymes known to be essential for the bacterium to cause disease, including anthranilate phosphoribosyl transferase (AnPRT; TrpD), the enzyme which catalyses the second committed step in tryptophan biosynthesis, isopropylmalate synthase (IPMS; LeuA), the enzyme which catalyses the first committed step in leucine biosynthesis, salicylate synthase (MbtI) which catalyses the production of salicylate, essential for the production of the siderophore mycobactin, and others. Through a combination of in silico modelling and in vitro assay, we have identified a set of weak AnPRT inhibitors, and are embarking on the structure-guided synthesis of more potent versions. We plan to use a similar approach with the other enzymes also, with the intention of producing useful anti- mycobacterial agents for the future. Host lipid-induced transcriptional regulation in M. tuberculosis. (Dr. Shaun Lott, Dr Sharon Kendall, Royal Veterinary College, London) We have recently showed that the essential transcriptional regulator KstR, which has previously been implicated in pathogenesis, directly controls the expression of many lipid metabolism genes in M. tuberculosis. Additionally, a similar transcriptional regulator, KstR2, has also been identified to control a smaller regulon. KstR and KstR2 both belong to the TetR family of transcriptional regulators, and our hypothesis is that the activation of KstR and/or KstR2 is triggered by lipid ligands derived from the human host, triggering bacterial adaptation to the intracellular environment. We are aiming to structurally and functionally characterise these transcription factors to discover more about their mode of action. Novel proteins from Orf virus. (Dr. Chris Squire, Professor Ted Baker, Prof. Andrew Mercer, Virus Research Unit, Otago University) Orf virus is an animal virus, and a member of the poxvirus family. Its genome sequence shows that in addition to the genes required for replication and assembly, it encodes genes for a large number of novel proteins that appear to have no counterparts in other organisms. We believe that many of these proteins are involved in infection, or in immune avoidance (by mimicking components of the host immune system). Some of these have potential therapeutic applications. We have carried out a preliminary bioinformatic survey, and identified a subset of these proteins that we predict to have important functions, and well defined structures. The aim is to express and purify the proteins, test their predicted functions and determine their 3D structures by X- ray crystallography. These scholarships are funded by research grants from the NZ Foundation for Research, Science & Technology, and include University Fees, working expenses and a stipend of NZ$25,000 p/a. Candidates should have a First or Upper Second Class Honours or Masters Degree or equivalent, and have a strong interest in using protein structure to elucidate biological function. Applicants should write to Dr Shaun Lott (s.l...@auckland.ac.nz) or Prof. Ted Baker (ted.ba...@auckland.ac.nz) in the first instance, enclosing a CV and an academic transcript, citing reference AGNRF1, by May 15th 2009. Informal inquiries are welcomed at the same addresses. Auckland was recently ranked joint 4th in the world in the Mercer Quality of Living Survey: http://www.mercer.com/qualityofliving#Top_5_ranking_cities_by_region More information about living & studying in Auckland can be found here: http://www.aucklandnz.com/ More information about the School of Biological Sciences at The University of Auckland can be found here: http://www.sbs.auckland.ac.nz/uoa/science/about/departments/sbs/about-us.cfm More information about Dr Shaun Lott’s Research Group can be found here: http://shaunlott.blogspot.com More information about Professor Ted Baker’s Research Group can be found here: http://lsb.sbs.auck
Re: [ccp4bb] Computer hardware and OS "survey"
These Greeks ... > However, the inhabitants of this planet seem to be quite fond of this OS That's because the inhabitants of this planet use computing machines mainly to play Doom & World of Warcraft ;-) But then it comes to using computers for actual computation, things change: ___ The representation of the various operating system families in the latest top500 list is²: Count Share (%) Linux 439 87.8 % <=== Windoze 5 1.0 % <=== Unix23 4.6 % BSD Based 1 0.2 % Mixed 31 6.2 % Mac OS 1 0.2 % Totals 500 100.0 % ___ Nicholas ² http://www.top500.org/stats/list/32/osfam -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] Computer hardware and OS "survey"
On May 3, 2009, at 12:03, Nicholas M Glykos wrote: Everything generally just works from the installers so I would say you are more likely to be able to just get on with your structure-related science on this OS that Linux. I tried to recall when was the last time that we determined a structure without having to write a single line of code, or without having to modify sources (and recompile). Guess what: never happened (and, hopefully, never will ;-) Nichola - you are a lucky man to have such fun with your structures. I am having a hard time trying to recall the last time I had to write a single line of code to solve a structure and I can most certainly ensure you that I have not compiled anything else than ARP/wARP (and this only in OSX) for the last 8-12 years. Most (if not all) structures we solve happen through GUIs and command lines. I am not a Windows fun and I do not even like Windows. However, the inhabitants of this planet seem to be quite fond of this OS, so this fact - right or wrong - cannot be ignored. There is no fundamental reason that crystallography cannot be done in Windows. I seem to recall - and please correct me if I am wrong - that Ralf has once posted that some phenix modules run faster in Windows than other systems. I was configuring yesterday a 399 Euro machine from "Plaisio" (I am on "vacation" in greece) for my niece and I installed PyMol on it - and - hey: it actually look very much Ok. And to be honest Vista is not as bad as most OSX forums think they are. Will I change my Mac then? No. Will I scrap the FC10 workstations at the lab and install Windows 7 or Vista? No. Does this mean that Windows is a useless OS? No. I guess this email was not very helpful and from this discussion I will keep the coconut shells trick that Bill reminded us ... ;-) Best - Tassos
Re: [ccp4bb] Computer hardware and OS "survey"
As this has not been cited, I decided to drop my opinion here. Since last year I have a system which I consider almost complete to my needs (good crystallography computing and precise office tools). With "precise" I mean completely compatible file formats to students and wherever I go/send a document of mine. Unfortunately I find OpenOffice not to be very 100 % compatible to MSOffice, eg, formulae, which is an issue for a physical chemistry lecturer (and evetually crystallography presentations). I might be outdated yet I am still at openSuSE 11.0, so no experience with OpenOffice 3.0. Also, to be questioned about the xml format, so it would be nice to have some reference here (questionable as well, why not to "force" students and whoever else to use open format documents?). With crossover, again problems with formulae. For these cases I use VirtualBridges' win4lin. It is still a bit slow in my laptop, but I wonder about these 4 GB memo machines nowadays. It seems to me it has a much easier way to exchange files between win and lin and use less machine resources than virtual machines; but I would like to hear from someone who has extensive experiences with both. Nevertheless, limitatons are that it is compatible with winXP and below only and I cannot tell about its speed for development. It is nice to use the 4 x 3 part of my wide screen to project the classes under XP, whilst on the remaining screen strand "top" shows me the several processes running on the backgrond! Together with hibernate, yet 20+ days without rebooting the computer (no processes stopped) and using linux and whatever needed within XP, just whenever needed. Other than that, crossover is very nice for "common" documents. For outlook (I cannot find a free alternative for the calendar with all functions therein), it is simply fine. I hope this might be useful for someone else. Jorge Prof. Jorge Iulek, Ph. D. Protein Purification and 3D Structure Determination Group Department of Chemistry State University of Ponta Grossa - PR Brazil e-mail: iulek at interponta dot com dot br iulek at uepg dot br * This is the first time I see a discussion about this issue in science. To Answer to Pete...KDE and Gnome are user friendly and ergonomic windowing systems and nowadays major Linux Distributions make using these MUCH easier than some years ago. We have both, OSX and Linux workstations in our lab, but for computational needs you would have to buy a Mac Pro workstation that is expensive compared to the PC counterpart. Else on cheaper iMacs you can not do heavy calculations, the system is not made for this. Desktop needs like grant writing are greatly improved now with openOffice and for Microsoft fans with wine + Microsoft Office. But in the end I really have to agree with Nicholas. People tend to stigmatize Linux as a user unfriendly and unusable system for every day tasks. This is completely wrong and it would be nice if people would give a try to good distributions like Suse 11.1 or Ubuntu, that are very easy to install and maintain. Best wishes. Peter On Sat, 2 May 2009 11:50:56 +0100, mb1pja wrote: .. but OSX gives you Unix AND you can run Word /Powerpoint without rebooting. And you get a user-friendly ergonomic windowing system that kicks the out of XP/Vista/KDE/Gnome... best wishes Pete On 2 May 2009, at 11:32, Nicholas M Glykos wrote: Dear All, We confuse scientific computing with the individual scientists' computing needs: just because a scientist has to write a grant application using word, does not make windows a platform suitable for scientific computing (or anything else for that matter). Using computing machines for doing science boils down to actually using computing machines to compute things, and for that you need a proper open-source, production-oriented, stable programming environment, ie. GNU/Linux. What individual scientists prefer for satisfying their desktop needs is interesting, but, at least to my mind, largely irrelevant. My twopence, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] Computer hardware and OS "survey"
> Everything generally just works from the installers so I would say you > are more likely to be able to just get on with your structure-related > science on this OS that Linux. I tried to recall when was the last time that we determined a structure without having to write a single line of code, or without having to modify sources (and recompile). Guess what: never happened (and, hopefully, never will ;-) Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
